Establishment and application of integrated platform for proteome quantification

Abstract

To improve the accuracy, throughput and automation of proteome quantification analysis, an integrated platform including a microflow mixed-bed ion exchange column, a hydrophilic immobilized enzymatic reactor (hIMER) and nanoRPLC-electrospray ionization (ESI)-MS/MS system was established. Online separation and digestion of dimethylated proteins, followed by peptide separation, identification and quantification can be realized automat ically by this platform. High and light dimethyl-labeled (H/L) proteins with the mass ratio of 1:1 were used to evaluate the quantification performance of the platform. The results showed that the dimethyl labeling efficiency at protein level was 90%. The incomplete digestion resulting from 10 min online digestion by the hIMER column and the non-specific adsorption of protein digests on the column had little adverse effect on the accuracy of protein quantification results. The mean value of H/L (mass ratio) of all the quantified proteins was 1.01. This platform was finally applied to analyze the different protein expression levels of two mice hepatocarcinoma ascites cell lines with high and low lymph node metastasis rates (Hca-F and Hca-P cell lines). Finally 15 up-regulated and 12 down-regulated proteins (Hca-F/Hca-P) were successfully obtained. All these results demonstrated that the integrated platform can be used for proteome quantification with the advantages of high accuracy and high throughput.